EDIT: I've added a video that displays the bug and how to reproduce it. It's 17 minutes long and I discover some stuff as I go, so you may wish to watch all of it. https://youtu.be/Tq6vy9xvMEg (deprecated)

After some thinking, it may not so much be an issue with the inserters, but with chest and wagon inventories instead and it's just the inserters where the symptoms show.

Hey.
I've been able to reliably reproduce a glitch with stack inserters loading a wagon.
The inserters will begin loading the wagon just fine, but at some point at least one of the inserters will simply not drop its item anymore, as though there was no space in the wagon anymore (there are most definitely multiple slots free).
The inserters have not been disabled during the process, and they were successful in the previous swing.
Changing anything at all will fix the issue: rotating any of that wagon's inserters by 180 degrees, removing or adding an item to the wagon, telling the wagon to leave, and dock anew. The only thing that does not seem to fix it is to add or remove an item to the chest the inserter is picking up from (but opening that chest does).

In the attached save is a somewhat complex loading/unloading system which can be used to reproduce the issue. Item loadouts are selected via circuitry and communicated to the loading contraption. New loadouts can be sent while the train is already in the station and the load will be adjusted accordingly - this is when the glitch happens maybe 70% of the time. I don't believe I have seen the glitch happen if the train freshly arrived. But after looking carefully, it does not appear to be the result of a faulty circuit. Instead the inserter(s) simply aren't releasing the item.
Changing the stack size to 1 from 12 makes no difference, the inserters still get hung up.

That said, depending of the timing of sending the new loadout, I have occasionally seen wrong values in my circuitry, so when it looks as though the inserters are just glitching again, you still need to check the wagon if there is any space in it. If there is, you have a glitch, if there isn't, it's probably just the circuitry plus bad timing causing a false positive along the way.

I'm entirely willing to move this to a screen share on discord to show you how I reproduce the issue (I live in Germany). The station is probably a pain to understand if you didn't build it and way too complex to explain in here. I'll be around for another hour before I head off to bed, you could send me a PM on discord if you wish: Charlie (gghf PaterFrog Eleeyah)#8931

I've improved the station further by giving the loading inserters falling edge detectors. This way you can be sure that any time the inserters hang, it's because of that strange glitch.
I still figure that the glitch itself is caused by inventory code, rather than inserters, but that the inserters show the symptoms.

Attached is another save. Please be aware that you may not always see red lamps from these glitches anymore, due to the circuitry I added. It's usually enough to open one of the requester chests to make the inserters go again. Sometimes you have to open a specific one.